SMTL ID : 8ts0.1

Crystal Structure of human ASGR1 CRD (Carbohydrate Recognition Domain) bound to 8M24 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: W.47, E.50, F.52, F.59, K.99 Chain B: F.96 Chain C: R.61, L.62 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Water bridges: C:R.61, B:T.94 Hydrogen bonds: A:E.50 GOL.2: 6 residues within 4Å: Chain A: V.93, Q.114, G.115, T.116, T.117 Chain B: G.41 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.115, A:T.117, B:G.41 Water bridges: A:Q.114, A:Q.114 GOL.3: 11 residues within 4Å: Chain A: F.175, P.176, V.178, S.186, L.187, S.188 Chain B: Q.160, S.162, S.176, S.177, T.178 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.162, B:S.176, B:T.178, A:F.175, A:S.186, A:S.188 GOL.4: 6 residues within 4Å: Chain A: D.102, Y.108 Chain B: Y.49, L.54, A.55, D.56 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.49, B:L.54, B:D.56, A:D.102 GOL.5: 8 residues within 4Å: Chain B: Q.37, K.39, K.45, P.59, R.61, F.62, E.81, D.82 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.37, B:K.39, B:K.39, B:K.45, B:K.45, B:R.61, B:D.82, B:D.82 GOL.9: 7 residues within 4Å: Chain C: Q.118, D.120, W.122, E.131, N.143, D.144 Ligands: CA.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.118, C:N.143, C:N.143

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain C: D.94, D.121, E.131, D.132 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.94, C:D.94, C:D.121, C:D.132, H2O.14 CA.7: 6 residues within 4Å: Chain C: Q.118, D.120, E.131, N.143, D.144 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.120, C:E.131, C:D.144, C:D.144 CA.8: 3 residues within 4Å: Chain C: V.69, E.75, E.156 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.75, C:E.75, C:E.156, C:E.156, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sampathkumar, P. et al., Targeted protein degradation systems to enhance Wnt signaling. Elife (2024)

Release Date

2024-06-19

Peptides

8M24 Fab Heavy chain: A
8M24 Fab Light chain: B
Asialoglycoprotein receptor 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

8M24 Fab Heavy chain

8M24 Fab Light chain

Asialoglycoprotein receptor 1